Devuan and Climate Cluster Milestone

Just a short note on some hardware status.

As of this moment, I’ve got 2 x Pi Model 2 boards, in the dogbone stack / case, running on a mostly built as I like it Devuan Jessie. My desktop at the moment is a similarly built Devuan, but with the hardware being my Pi Model 3. That’s a total of 12 cores available for use in a cluster formation.

They all have distcc installed (though not yet configured) so I can now do compiles of code spread over many cores. But I’ve set it up before, so configuration won’t take long.

All of them were made from a NOOBS base installation of Raspbian, then upgraded to Devuan.

I then ran the script that I’m including below. Note that many bits are commented out. Some of them I just didn’t want on these systems (like a VNC remote terminal). You can customise this list to suit your needs. For example, I’ve got gfortran and distcc stuff in it. If you are not going to be doing big compiles or FORTRAN on your system, you don’t need them.

Here’s the “disk” (chip) usage:

Filesystem     1K-blocks     Used Available Use% Mounted on
/dev/root       15951288 10406200   4711760  69% /
devtmpfs          469532        0    469532   0% /dev
tmpfs              94776      416     94360   1% /run
tmpfs               5120        4      5116   1% /run/lock
tmpfs             189540    47624    141916  26% /run/shm
/dev/mmcblk0p6     67434    20698     46736  31% /boot
/dev/mmcblk0p9  13157084    34988  12430692   1% /Climate
/dev/mmcblk0p8     67434        0     67434   0% /boot0
/dev/mmcblk0p5     30701     1563     26845   6% /SETTINGS
cgroup                12        0        12   0% /sys/fs/cgroup
cgmfs                100        0       100   0% /run/cgmanager/fs
tmpfs              94776        0     94776   0% /run/user/1000

Note that I have this on a 32 GB “chip” (mini-SD card) and have it set up with a /Climate directory where I’m presently working on GISS GSM Model II. Don’t let the size of “/” worry you. I had to dump a 6 GB USB thumb drive into that for a different use… The actual install takes about 6 GB and it fits on an 8GB ‘chip’ if you don’t make a /Climate directory. (One of the Headless nodes is using an 8, the other a 16, this workstation node has a 32 since this is where source and compiled bits will live.)

There is still a fair amount of configuration to do since I made these from the ground up. Things like turning on distcc, enabling ssh so I can remote log in (just found that out when I brought them up headless…) making sure they are booting with fixed IP (right now, one is, the other isn’t) and have a set name (“Headless1” and “Headless2” are now set). That kind of stuff.

One big bit I need to do: These by default boot up live with a GUI open as user Pi. I want to have a login prompt that asks for a password AND my “usual and customary” login name and home directory… So that is yet to do.

I tried to do a Linpack performance benchmark, but it would reach 396% of CPU and hang. That was on a Debian SystemD chip, so I hope it doesn’t hang on these. (It was after that I ‘moved on’ to doing the cluster build).

The boards are just plugged into the ethernet ports on my interior WiFi router for now. As the Pi is only 10 / 100 Mb Ethernet, that Netgear router is plenty fast for them. When I go over 4 (IF I go over 4) I’ll need to fire up my 8 port Netgear Switch…

Moving Forward

I’m now in a position to try running the Model II GCM code, and then I can start looking at Model E (that has distributed MPI already coded into it). If needed, I can put similar changes into Model II and make it distributed execution (though I’d rather not just yet).

Most importantly, I can make some needed tests of MPI function and efficiency. OpenMP (thread parallel) was dismal in an earlier test on Debian, it actually ran slower! Hopefully MPI (MPICH2 – core parallel) will actually have speed increases…

Essentially, I have my Toy Cluster built and ready to play with, test, and characterize. I think it will be doing “interesting things” by Sunday. (Spouse has spoken for Saturday as Macintosh Fixing Day… new disk, load data, etc…)

So far there is only one “bug” I’ve seen in this release of Devuan. When you choose to logout, it gives a panel with choices of “shutdown” and “exit to prompt” or some such. Shutdown doesn’t work, so you must chose the exit to terminal line prompt. That then doesn’t give you a terminal line, but another panel where shutdown does work… Petty annoyance, so might take a while for Devuan to fix on the Pi.

Overall, I’m quite happy with it, and I’m very happy to be done with the long search for a way out of systemD hell.

The Build Script

Here’s my “build script” for the Devuan installation. As is my custom, I make one of these for any build I expect to do more than once. It references earlier postings on the earlier steps (doing a Debian installation) and points at the reference for the Debuan upgrade that I found most useful (when making my first Devuan chip in the article here )

The Script:

root@raspberrypi:/media/pi/PINK_ext4/Pi_Config_Files# cat BuildDevuan 
echo " "
echo "Do the NOOBS install: "
echo " "
echo " https://www.raspberrypi.org/help/noobs-setup/ "
echo " "
echo "Do the Raspbian installation.  Then copy this script from an external SD"
echo "card or USB drive into your working directory (home directory or /media/data"
echo "after all the usual and customary NOOBS setup questions are answered and done."
echo " "
echo "Make sure you select the USA keyboard if in the USA, default is UK!"
#
# In general, I'm encapsulating what all I did in these two postings as a script:
#
# https://chiefio.wordpress.com/2015/07/18/raspberry-pi-m2-unboxing-and-setup/
#
# https://chiefio.wordpress.com/2015/07/22/raspberry-pi-software-setup/
#
# If you didn't already change the password while running NOOBS,
# When done, log in as 'pi' password 'raspberry'.  Change the password.
# passwd
# and respond with the new one when prompted.

echo ""
echo "Do the upgrade / change to Devuan from this posting:"
echo ""
echo "https://git.devuan.org/dev1fanboy/Upgrade-Install-Devuan/wikis/Upgrade-to-Devuan-and-minimalism"
echo " "
echo "It basically consists of changing /etc/apt/source.list to have:" 
echo ""
echo "deb http://packages.devuan.org/merged jessie main"
echo ""
echo "as the only active line. Then do:"
echo "apt-get update"
echo "ignore the error message about keyrings and signatures, you don't have it yet."
echo "apt-get install devuan-keyring"
echo "Now you have the keyring... and can do another apt-get update if you want one"
echo "with no error messages, but it doesn't matter."
echo ""
echo "apt-get install sysvinit-core"
echo "apt-get install base-files"
echo "That last one may say you are already up to date."
echo "The next one will kill Berry Boot images with an attempted kernel swap."
echo "apt-get dist-upgrade"
echo "apt-get autoremove --purge"
echo "# apt-get autoclean"
echo ""
echo "Now reboot to start running Devuan properly.  If you don't have xfce, add it"
echo ""
echo "apt-get install xfce4"
echo "and startxfce runs it." 
echo ""
echo "Also, to change the name of your machine, edit /etc/hostname and make it"
echo "what you like.  "
echo "Here, I'm going to just set mine by brute force write to the file."
echo " "
echo "echo 'Devuan_armhf' > /etc/hostname "
echo " "

echo 'Devuan' > /etc/hostname 

echo " "
echo "Next, do the 'usual' update upgrade that brings you up to the present"
echo "repository status (need a network connection from here on out)"
echo " "
echo "You can either put 'sudo' in front of each of these commands, or just "
echo "'become root' which is what I usually do."
echo " "
echo "sudo bash"
echo " "
echo "then run this script with ./BuildIt (assuming you didn't change the name"
echo "and that you are 'in' the directory where it is located.)"
echo " "
echo "apt-get update"
echo "apt-get upgrade"
echo " "

#apt-get update
#apt-get upgrade

echo " "
echo "Start doing useful operational 'packages'. "
echo " "

# This gets the useful tools like "nslookup" for looking at Domain Names

echo " "
echo apt-get install dnsutils
echo " "

#apt-get install dnsutils

echo " "
echo " VNC is a nice way to get a remote desktop.  It takes some configuring later."
echo " "

echo " " 
echo apt-get install tightvncserver
echo " "

#apt-get install tightvncserver

echo " "
echo "I like wicd for an easier way to manage wireless devices and networks."
echo " "

echo " " 
echo apt-get install wicd
echo " "

#apt-get install wicd

echo " "
echo "Scrot is a tool for taking screen shots by saying 'scrot' in a terminal"
echo " "

echo " " 
echo apt-get install scrot
echo " "

#apt-get install scrot

echo "Normally I would install 'build-essential' to get things like C compiler"
echo "and some language tools, but they were already installed on the R.PiM2."
echo "Now I add gfortran and distcc"

#apt-get install build-essential

apt-get install gfortran distcc distcc-pump dmucs ccache doc-base gfortran-4.9-doc libgfortran3-dbg

echo " "
echo "Some 'user land' useful things like browser options and Office / Mail tools."
echo " "
echo "Chromium is the 'chrome' browser from Google but in Linux land"
echo " "
echo "    CHROMIUM is installed by default now"

echo " " 
echo apt-get install chromium
echo " "

#apt-get install chromium

# IceApe is a "more free" version of IceWeasel that is a "more free" version of
# Firefox that is a rebranded Mozilla that is...   IceDove is the matching
# Thunderbird replacement minus the trademarks, non-free bits, etc.

echo " "
echo "Doing IceApe browser and IceDove mail reader"
echo " "

echo " " 
echo apt-get install iceweasel
echo apt-get install icedove
echo " "

apt-get install iceweasel
apt-get install icedove

echo " "
echo "GIMP is the photo editor ( 'photoshop Free'...) "
echo " "

echo " " 
echo apt-get install gimp
echo " "

apt-get install gimp

echo " "
echo "Don't forget Libreoffice - Microsoft?  We don't need no steenking MicroSoft..." 
echo " "

echo " " 
#echo apt-get install libreoffice
echo "Already installed by default"
echo " "

#apt-get install libreoffice


# I tried "arora" and got error messages and "xbmc" was not working for sound
# so I'm not installing those again until it's clear they work.  Arora is a
# browser (so who needs "yet another browser" with Epiphany in by default and
# with both IceApe and Chromium installed?...) and I'll likely make a dedicated
# SD card for the media center option as there are 2 Pi Model 2 version up
# and I won't need to screw around with Debian issues...
#apt-get install arora
#apt-get install xbmc

# As I also wanted one of these to be a bittorrent server, I sometimes add
# the "transmission" bittorent code.

echo " "
echo "Adding the 'transmission' bit torrent server"
echo " "

echo " " 
echo apt-get install transmission
echo " "

apt-get install transmission

echo " "
echo "To get NTFS disks (like USB or an NTSB formatted SD card in adapter) to "
echo "work 'read write' instead of just 'read only', you need ntfs-3g"
echo " "

echo " " 
echo apt-get install ntfs-3g
echo " "

apt-get install ntfs-3g

# In Theory, this installed 2 VNC "viewers" so the R.Pi could use VNC to 
# get to other machines.  In practice, I found that one of them locked up
# my console when launched against my own machine as target (might be a 
# PIBKAC problem - Problem Is Between Keyboard And Chair - as the R.Pi
# isn't really expecting to drive 2 video sessions at once (the real one
# and the VNC one inside the real one...) so maybe all is fine and I just
# need to RTFM (Read The, er, "Friendly" Manual) before using software...

echo " "
echo "Some VNC Viewers for being the client instead of the server"
echo "I've not used either of these yet so have no clue about them in practice"
echo " "


echo " " 
echo apt-get install xtightvncviewer
echo apt-get install ssvnc
echo " "

#apt-get install xtightvncviewer
#apt-get install ssvnc

echo " "
echo "Want an NFS (Network File System) server so you can share disks with" 
echo "your internal network?  This will install the code, then you get to" 
echo "configure things like /etc/exports"
echo " "


echo " " 
echo apt-get install nfs-kernel-server
echo " "

apt-get install nfs-kernel-server

# prior to first use.  Or reboot.

# In your /etc/exports file, put something like:

# /etc/exports: the access control list for filesystems which may be exported
#		to NFS clients.  See exports(5).
#
# Example for NFSv2 and NFSv3:
# /srv/homes       hostname1(rw,sync,no_subtree_check) hostname2(ro,sync,no_subtree_check)
#
# Example for NFSv4:
# /srv/nfs4        gss/krb5i(rw,sync,fsid=0,crossmnt,no_subtree_check)
# /srv/nfs4/homes  gss/krb5i(rw,sync,no_subtree_check)
#

# /YourFileSystem  *(rw,sync,fsid=0,no_root_squash)
# But without the # in front of YourFileSystem... and with your file system...

echo " "
echo "IF you chose that 'add a 512 MB partition option' at build time"
echo "This adds it to the /etc/exports file so it is NFS mountable elsewhere"
echo " "
echo "echo '/media/data   *(rw,sync,fsid=0,no_root_squash,no_subtree_check)' >> /etc/exports"
echo " "

#echo "/media/data   *(rw,sync,fsid=0,no_root_squash,no_subtree_check)" >> /etc/exports

# Remember to do a 

echo " "
echo "Restarting the appropriate services so NFS will work"
echo " "
echo " " 
echo service rpcbind restart
echo service nfs-kernel-server restart
echo " "

service rpcbind restart
service nfs-kernel-server restart

# I also made my box a static IP number as it's a server.  You will need to
# make this your own server name and IP numbers.
#
# Here's my /etc/network/interfaces file with leading # to make it comments.
# 
# I will make this a "dump these lines in to replace" in my running version.
#

echo " "
echo "Remember to make your /etc/network/interfaces file have a static IP#"
echo "If you are going to be using PXE boot and such"
echo " "

#auto lo
#iface lo inet loopback

#auto eth0
#allow-hotplug eth0
#iface eth0 inet static
#address 172.16.16.253
#netmask 255.255.255.0
#gateway 172.16.16.254
#dns-domain chiefio.home
#dns-nameservers 172.16.16.254 192.168.1.253 192.168.1.1
#
#auto wlan0
#allow-hotplug wlan0
#iface wlan0 inet manual
#wpa-conf /etc/wpa_supplicant/wpa_supplicant.conf
#
#auto wlan1
#allow-hotplug wlan1
#iface wlan1 inet manual
#wpa-conf /etc/wpa_supplicant/wpa_supplicant.conf

# Don't forget to do a
# ifdown eth0
# wait a minute for it to quiet down
# ifup eth0

# As I want this to be a DNS server, DHCP server, and PXE server (uses a 
# tftp or "Trivial File Transfer Protocol" server, all of those can come in
# one package with dnsmasq.

echo " "
echo "Installing a light weight but effective DNS, DHCP and TFTP service"
echo " "

echo " " 
echo apt-get install dnsmasq 
echo " "

apt-get install dnsmasq 

echo " "
echo "Yes, it takes configuring.  See the file at"
echo " /etc/dnsmasq.conf"
echo " "

# Then I installed the Apache web server :

# http://www.raspipress.com/2012/09/tutorial-install-apache-php-and-mysql-on-raspberry-pi/

echo " " 
echo "Instlling the Apache Web Servier and related stuff"
echo " "

echo " " 
echo apt-get install apache2 apache2-utils apache2-doc
echo " "

apt-get install apache2 apache2-utils apache2-doc

# and yes, it takes some configuring and even web page building.
# See files in places like /etc/apache2/sites-available and more.

echo " " 
echo apt-get install libapache2-mod-php5 php5 php-pear php5-xcache
echo " "

apt-get install libapache2-mod-php5 php5 php-pear php5-xcache

echo " " 
echo apt-get install php5-mysql
echo " "

apt-get install php5-mysql

echo " " 
echo apt-get install mysql-server mysql-client
echo " "

apt-get install mysql-server mysql-client

# These needed to be added for Transmission and for file systems

apt-get install transmission-daemon
apt-get install btrfs-tools xfsprogs gparted f2fs-tools unionfs-fuse
apt-get install hfsplus hfsutils
apt-get install squashfs-tools aufs-tools


#
echo " "
echo "And that's the end of my present install build process."
echo " "
#
# There are several files to edit and configure.  Eventually I'll add a 
# "here script" to dump them from this script to where they belong, or 
# I'll just save a copy and have a 'save / restore' copy process.
#
# Once I get everything configured ;-)

Folks may notice this looks mostly the same as the Debian build script. Some things commented out. Some added. A few, like iceape, removed since there is not target for it to build anymore.

For anyone looking to get a working Devuan on a Pi, with most of the goodies needed to do interesting things, this ought to get you there.

FWIW, it took me about 5 hours from start to end. (Part of the duration will depend on network speed… especially that part where the apt-get dist-upgrade says to go get a cup of coffee…) I made copies of the chip at the NOOBS installed stage, at the Devuan raw upgrade, and after my scripted added packages. (dd bs=10M if=/dev/sd{your drive letter} of=/where/you/save/it) using the 8 GB chip for the basic build, so less to store. Then later did a similar dd from the final saved image onto the 16 GB chip. That leaves about 8 GB not allocated, so with gparted you can make that /Climate partition…

During much of that time you can be doing other things. Do realize that during the Devuan upgrade it does prompt a couple of times, and at one point tosses you into a log file reader. I think I did :q to get out of it by vi instinct, and who knows what the proper exit command is… so it isn’t entirely ‘fire and forget’, but more like “fire and check back”.

Now, with my saved chip images, I can skip all that in the future and dd it onto any new chips I want to make, then modify the config.

With that, it’s time for a break! Happy Hacking!

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